Contacts of the helix formed by residues 136 - 148 (chain B) in PDB entry 2QVH
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 136 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134B ALA 4.2 0.6 + - - -
135B TRP* 1.3 78.2 - - - +
137B VAL* 1.3 64.5 + - - +
138B ASP* 3.3 24.1 + - - +
139B THR* 2.6 41.8 + - - -
140B ALA* 3.0 18.7 + - - +
159B CYS* 3.8 2.0 - - - -
164B GLU* 4.0 11.0 - - - +
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Residues in contact with VAL 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B ASP* 1.3 75.2 + - - +
138B ASP* 1.3 63.4 + - - +
140B ALA* 3.3 2.4 + - - +
141B VAL* 2.9 29.5 + - + +
159B CYS* 3.9 6.2 - - - -
164B GLU* 3.7 45.4 + - + +
167B GLU* 3.6 27.6 - - + +
168B VAL* 4.0 12.3 - - + +
171B ARG* 3.1 26.7 - - - +
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Residues in contact with ASP 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B ASP* 3.3 12.5 + - - +
137B VAL* 1.3 77.5 - - - +
139B THR* 1.3 64.1 + - - +
141B VAL* 3.3 5.1 + - - +
142B ARG* 3.1 26.7 + - - +
171B ARG* 3.1 28.6 + - - +
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Residues in contact with THR 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B GLU* 3.7 20.9 - - - +
135B TRP* 3.6 29.8 - - + -
136B ASP* 2.6 25.9 + - - -
138B ASP* 1.3 76.8 - - - +
140B ALA* 1.3 57.6 + - - +
142B ARG* 3.4 23.6 + - - +
143B MSE 2.9 34.3 + - + +
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Residues in contact with ALA 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B TRP* 3.7 25.1 - - + +
136B ASP 3.0 19.2 + - - +
137B VAL 3.6 4.0 - - - +
139B THR* 1.3 77.8 - - - +
141B VAL* 1.3 55.9 + - - +
144B ILE* 2.8 40.5 + - + +
158B PRO* 4.0 10.3 - - + -
159B CYS* 3.9 18.6 - - - -
168B VAL* 4.0 8.5 - - + -
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Residues in contact with VAL 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B VAL* 2.9 24.4 + - + +
138B ASP 3.3 7.2 + - - +
140B ALA* 1.3 76.0 - - - +
142B ARG* 1.3 59.2 + - - +
144B ILE* 3.6 2.0 + - - +
145B ARG* 3.1 72.5 + - - +
168B VAL* 4.4 11.7 - - + -
171B ARG* 3.6 43.3 - - + +
172B VAL* 4.1 14.8 - - + +
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Residues in contact with ARG 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B GLU* 3.6 26.5 + - - -
138B ASP* 3.1 10.3 + - - +
139B THR* 3.4 31.5 + - - +
141B VAL* 1.3 77.9 - - - +
143B MSE 1.3 96.0 + - + +
145B ARG* 3.2 12.5 + - - +
146B LEU* 2.9 34.7 + - + +
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Residues in contact with MSE 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B GLU* 3.8 33.9 - - - +
110B ASP* 6.3 1.6 - - - -
111B VAL* 5.5 4.9 - - - -
135B TRP* 3.6 37.9 - - + -
139B THR* 2.9 33.1 + - + +
140B ALA 4.0 0.2 - - - +
142B ARG* 1.3 102.3 - - + +
144B ILE* 1.3 61.5 + - - +
146B LEU* 3.2 36.3 - - + +
147B LEU* 2.8 44.6 + - + +
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Residues in contact with ILE 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B ILE* 5.0 1.3 - - + -
135B TRP* 4.8 6.3 - - + -
140B ALA* 2.8 27.4 + - - +
141B VAL 3.9 3.4 - - - +
143B MSE 1.3 76.3 - - - +
145B ARG* 1.3 58.9 + - + +
147B LEU* 3.9 4.4 - - - -
148B ASP* 3.0 27.7 + - - +
152B LEU* 4.3 4.5 - - + +
155B VAL* 3.9 36.8 - - + -
158B PRO* 4.4 4.9 - - + -
168B VAL* 3.8 28.0 - - + -
172B VAL* 4.0 15.9 - - + -
174B VAL* 3.7 31.2 - - + -
176B ILE* 4.0 7.4 - - + -
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Residues in contact with ARG 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B VAL* 3.1 39.6 + - - +
142B ARG* 3.5 11.1 - - - +
143B MSE 3.2 0.4 - - - -
144B ILE* 1.3 76.9 - - + +
146B LEU* 1.3 66.0 + - + +
148B ASP* 3.3 16.9 + - - +
149B ARG* 4.0 4.0 + - - +
171B ARG* 3.1 38.2 + - - +
172B VAL* 4.6 7.3 - - + +
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Residues in contact with LEU 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B VAL* 5.4 10.3 - - + -
142B ARG* 2.9 18.2 + - + +
143B MSE 3.2 35.2 - - + +
145B ARG* 1.3 79.0 - - + +
147B LEU* 1.3 65.1 + - + +
148B ASP 3.3 0.7 + - - -
149B ARG* 3.4 42.2 + - - +
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Residues in contact with LEU 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B VAL* 4.6 11.0 - - + -
110B ASP* 4.3 3.1 - - + -
111B VAL* 3.7 42.8 - - + +
114B VAL* 4.0 19.2 - - + +
129B ILE* 3.8 24.0 - - + -
135B TRP* 4.1 17.7 - - + -
143B MSE 2.8 29.2 + - + +
146B LEU* 1.3 69.7 - - + +
148B ASP* 1.3 56.1 + - - +
149B ARG 3.0 10.7 + - - -
150B PHE* 3.1 29.4 + - + +
152B LEU* 3.9 22.5 - - + +
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Residues in contact with ASP 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B ILE 3.0 20.5 + - - +
145B ARG* 3.7 9.6 - - - +
146B LEU 3.2 1.4 - - - -
147B LEU* 1.3 73.0 - - - +
149B ARG* 1.3 59.8 + - - +
150B PHE 2.8 6.1 - - - -
151B GLU* 3.1 16.2 + - - +
152B LEU* 3.0 31.0 + - + +
173B SER* 5.7 2.8 - - - -
174B VAL* 3.5 28.6 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il